Environment ministry mandarins were among those who used the default settings on Google Groups, which allow public access to discussion threads, instead of limiting them to members only.
The mass-selling Yomiuri Shimbun said it found more than 6,000 cases where information from public or private organisations, including hospital records, was publicly available.
The Yomiuri, the world's biggest-selling newspaper, also admitted its journalists had been using the wrong settings on Google Groups, and may have revealed draft stories and interview transcripts to anyone who wanted to see them.
The user who sets up the group can determine who can join the group and who can view and post messages.
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The default on the set-up page allows anyone to see messages, although this can be limited by a drop-down menu.
A spokesman for the environment ministry admitted officials have used the service to share information, including planned talking points for negotiations on an international mercury trade treaty.
The Japanese delegation also uploaded its exchanges with their Swiss and Norwegian counterparts. The treaty is expected to be signed in the autumn.
The memos were not "top secret", but were not for public release, the spokesman admitted.
Officials from at least six government ministries and agencies used the wrong settings on Google Groups, allowing outsiders to see internal exchanges, national broadcaster NHK said.
The Yomiuri also reported that hospitals and schools had uploaded patients' and students' records.
At least one political party also used the service, revealing a list of its supporters, the Yomiuri said.